Status
v1.1 (September 2010):The Rhodotorula graminis strain WP1 genome sequence assembly v1.0 was built with the Arachne assembler from whole genome shotgun and paired end sequencing reads. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses.Note that the v1.1 data is a reannotation of the v1.0 assembly, but using newly available EST data for gene modeling and annotation.
Summary statistics for the Rhodotorula graminis strain WP1
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 21.01 |
| Sequencing read coverage depth | 8.55x |
| # of contigs | 323 |
| # of scaffolds | 26 |
| # of scaffolds >= 2Kbp | 25 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 1.42 |
| # of gaps | 297 |
| % of scaffold length in gaps | 1.1% |
| Three largest Scaffolds (Mbp) | 2.37, 1.72, 1.61 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome | Notes |
| EstClusters | EstClusters* | 19126 | 6692 | 35.0% | JGI cluster consensus sequences
for the JGI 454 ESTs |
| Ests | ESTs* | 1880475 | 844124 | 44.9% | 454 ESTs sequenced by JGI |
| *The Est data appear to contain contamination from a different species, possibly switchgrass; this is the likely cause of the low % mapping to the genome for this data | |||||
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 2126 | 1773 |
| transcript | 1585 | 1308 |
| exon | 254 | 155 |
| intron | 105 | 79 |
| description: | ||
| protein length (aa) | 501 | 407 |
| exons per gene | 6.24 | 5 |
| # of gene models | 7283 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL
Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.
Front Microbiol. 2015;6():978. doi: 10.3389/fmicb.2015.00978
Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL
Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.
Front Microbiol. 2015;6():978. doi: 10.3389/fmicb.2015.00978
Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
